Location: Corn Insects and Crop Genetics Research
Project Number: 5030-22000-017-21
Start Date: Sep 01, 2011
End Date: Aug 31, 2016
Molecular genetic markers that detect variation at single nucleotide polymorphisms (SNPs) within the European corn borer genome have been developed at the USDA-ARS CICGRU laboratory in Ames, Iowa. Assays that detect SNP marker variation are adapted for use on a Sequenom MassARRAY system located at the Center for Plant Genomics at Iowa State University (ISU-CPG; located in proximity to the CICGRU laboratory). Since assay materials are already available for use in the CICGRU laboratory, this project will incur nominal additional cost to ARS. DNA samples have already been prepared for European corn borer collected at the North American sites of North Platte, NE, Crawfordsville, IA, Monmoth, IL, Frankfort, IN, Bowersville, OH, and Oak Corners, NY. Collaborators in Europe have already provided DNA extracts from Rzeszów, Poland, Csongrad, Hungary, and Krasnodar, Russia. Additionally, collaborators in France will be providing DNA samples from 17 collection sites (estimated ship date to CICGRU is July 2011). A total of 178 SNP markers will be used to genotype all European corn borer samples using the Sequenom MassARRAY at the ISU-CPG, and resulting data will be received by the CICGRU for statistical analyses. Initial criteria for screening markers will include the determination of Hardy-Weinberg Equilibrium (HWE), with deviations calculated by chi-square tests between observed and expected heterozygosities. SNP markers that are in HWE will be used to estimate hierarchical population genetic parameters (Fst, Fis, and Fit), and exact tests for population differentiation using GENEPOP4.06 analysis software. Geographic structuring will be assessed using the isolation by distance (IBD) model that tests for correlation between Log of geographic distance between collection sites (in kilometers) and the parameter (Fst/(1-Fst)), and by principal component analysis to estimate other factors that influence genotypic variance among populations. Furthermore, the program STRUCTURE2.1 will be used to indicate the level of co-ancestry between genotypes from collection sites, and estimate the number of distinct breeding populations, level of population subdivision, and rate of migration (genetic exchange) within the European corn borer populations.